Changes in version 1.4.0 (2024-10-30)                  

  - gridDensity() now supports hexagonal grids.
  - Make 'grid.length.x' = 100 by default in gridDensity() and remove
    the default value for 'ngrid.x'.
  - New functions plotGrid() and gridSPE()
  - gridSPE() has an option to calculate grid-level count matrix for
    each cell type
  - Remove redundant argument 'n' in plotSpatial()
  - Rename 'coi' to 'contour', 'all' to 'self.included' in
    plotCellCompo()
  - Fixed a bug in plotContour() where 'overlay' is not working properly
  - Fixed a bug in corDensity() that produced NaN values
  - New argument 'contour' in allocateCells() allowing user to specify
    the contour levels for cell allocation. Default to all detected
    contours.
  - corDensity() can be run without running findROI(), and it returns a
    DataFrame instead of a list of DataFrames if no ROI detected.
  - New argument 'probs' added to plotDensity() for grid filtering when
    ROIs are not identified previously.
  - 'equal.cell' is set to TRUE by default in getContour().
  - plotContour() now plots contour for all the cells when 'coi' is NULL
    (by default).
  - When 'coi' contains multiple cell types, plotContour() looks for the
    corresponding contour in spe@metadata for plotting.
  - Added another option 'none' for 'overlay' in plotContour().
  - For multiple 'coi', getContour() now includes all coi in the contour
    labelling.
  - gridDensity() returns an extra column 'density_overall' in
    spe@metadata$grid_density.
  - plotDensity() plots overall cell density by default.
  - The default value of 'probs' in plotDensity() is now 0.5.
  - For multiple 'coi', plotDensity() now plots the total instead of
    average.
  - Fixed a ggtitle() bug in plotDensity() when 'coi' contains more than
    one cell type.
  - findROI() now use all cells (overall) by default.
  - coord_fixed for both plotDensity() and plotROI().
  - plotROI() now plots all the cells in the background when 'roi' is
    'overall'.
  - In corDensity(), 'trace' is now set to FALSE by default.
  - Fixed a bug in cellsInRegion() when there is only one ROI.
  - Fixed bugs in contour2sf() when no 'areas_up'.
  - Converted cell numbers as a vector in spe2PB().
  - Fixed a bug in spe2PB() when the count table from spe is not matrix.
  - Fixed a bug in plotContour() to ensure exact match for cell types to
    avoid similar cell type names.

                 Changes in version 1.2.0 (2023-10-30)                  

  - Bioconductor release.

                       Changes in version 0.99.0                        

  - Initial submission to Bioconductor.